My wife and I found this cool old version of MasterMind at Half Price Books - all the pieces were there, but the smaller black and white pegs were weirdly hard to pick up and kept rolling all over the place. This is just a simple tray to keep them contained, designed to fit snugly in the box, and there are curved edges on the inside of the tray to make it just a little easier to grab the pieces.

I printed this in black PLA with a .4mm nozzle, but I think you could likely print with a larger nozzle to get it done more quickly, and without much loss of quality.

You can find the model here on OnShape, in case you'd like to tweak it for other uses.